msprep2: Converts long state entry data into a format suitable for...
In stulacy/RDES: Utility Functions for Parametric Multi-State Models

Description Usage Arguments Details Value Examples

View source: R/msprep2.R

This function performs the same role as msprep from the mstate package, except that it accepts long data (each row corresponds to a state entry) rather than the wide format used by msprep (each row represents an individual with state entry indicated in columns).

msprep2(
  entry,
  tmat,
  censors = NULL,
  start_times = NULL,
  start_states = NULL,
  covars = NULL,
  idcol = "id"
)

`entry`	Long data frame of format `id` \| `state` \| `time`. State can either be character, with the same state names used in `tmat`, or integer where they refer to the rownumber of that state in `tmat`. Note that the `state` and `time` fields must be labelled this way.
`tmat`	Transition matrix in the standard format required by `msprep`.
`censors`	A long data frame with 2 columns, `id` and `censor_time`. Gives the last follow-up time for individuals that haven't entered a sink state.
`start_times`	A long data frame with 2 columns, `id` and `start_time`. Gives the time at which the patient entered the simulation. Defaults to 0.
`start_states`	A long data frame with 2 columns, `id` and `start_state`. Gives the state the patient entered the simulation in. Defaults to 1.
`covars`	Data frame where each row corresponds to an individual and details their covariate values. Must contain the id column specified in `idcol` alongside any covariate fields of interest.
`idcol`	The column that indexes these patients, must be present in `entry` and `censors`, `start_times`, `start_states`, and `covars` if supplied.

The long data format required by msprep2 is a more natural way of organising state entry data than the wide format required by msprep. An additional benefit of having the state entries organised in this fashion is that it allows for the situation where an individual enters the same state multiple times, which is not supported by msprep.

An object of class msdata, representing the transition data in long format.

 library(multistateutils)
 library(mstate)

 tmat <- trans.illdeath()
 entry <- data.frame(id=c(1, 2, 2),
                     state=c(2, 2, 3),
                     time=c(23, 35, 360))

 msprep2(entry, tmat)